Setup R env. Load packages and set default image export formats, size and resolution.
knitr::opts_chunk$set(echo = TRUE,
fig.height = 8,
fig.width = 8,
dev = c("png", "pdf"),
dpi = 1000)
library(tibble)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(reshape2)
library(ggplot2)
library(ggpmisc)
## Loading required package: ggpp
##
## Attaching package: 'ggpp'
## The following object is masked from 'package:ggplot2':
##
## annotate
library(ggtext)
library(RColorBrewer)
library(ggpubr)
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(htmlwidgets)
options(scipen = 999) #Prevent scientific notation
xlim.min <- 0
xlim.max <- 15
ylim.min <- 0
ylim.max <- 15
scatter_plot <- function(df, title="", tag="", text.scale=1) {
x.name <- paste("Transcript.",title, sep='')
y.name <- paste("Protein.",title, sep='')
df <- df[, c("Name", "top_hit_id", "top_hit_evalue", "top_hit_description",
y.name, x.name)
] %>%
mutate(Protein_Abundance_log = log2(get(y.name)+1)) %>%
mutate(Transcript_Abundance_log = log2(get(x.name)+1))
print("")
print(paste("Plotting matrix with",nrow(df),"rows using rows",x.name,",",y.name))
p <- ggplot(df,aes(x=Transcript_Abundance_log, y=Protein_Abundance_log)) +
geom_point(aes(label=Name, label2=top_hit_id, label3=top_hit_evalue, label4=top_hit_description),
size=1*text.scale) +
stat_poly_line(se=FALSE, col="red", formula = y ~ x) + # Add trend line
stat_poly_eq(mapping = use_label(c("n", "R2", "eq")), label.y = 0.95, label.x = 0.05, size=5*text.scale) + # Add equation
scale_x_continuous(limits=c(xlim.min, xlim.max), expand = c(0, 0), breaks = seq(xlim.min, xlim.max, by = 1)) +
scale_y_continuous(limits=c(ylim.min, ylim.max), expand = c(0, 0), breaks = seq(ylim.min, ylim.max, by = 1)) +
labs(title = title,
x = 'Transcript Expression [log2(TPM+1)]',
y = 'Protein Expression [log2(normalized abundance+1)]',
tag = tag) +
theme_light() +
theme(text = element_text(family="Helvetica"),
plot.title = element_text(size=20*text.scale, face="bold", hjust=0.5),
plot.tag = element_text(size=32*text.scale, face="bold"),
axis.title.x = element_text(size=16*text.scale),
axis.title.y = element_text(size=16*text.scale),
axis.text = element_text(size=14*text.scale),
axis.line = element_line(color="black", linewidth=0.4*text.scale),
axis.line.x = element_line(color="black"),
axis.ticks = element_line(color="black"),
aspect.ratio=1) # Make plot square
return(p)
}
names <- read.table("Mcapitata_V1_proteomic_data.tsv", sep="\t", header=TRUE, quote="", fill=FALSE, comment.char = '')[,1]
df <- read.table("Mcapitata_V1_multiomics_results.tsv", sep="\t", header=TRUE, quote="", fill=FALSE, comment.char = '')
dim(df)
## [1] 63227 55
df <- df[df$Name %in% names,]
dim(df)
## [1] 4036 55
text.scale <- 0.3
T1_Amb_1603 <- scatter_plot(df, "MC.289_T1.Amb_1603", "A", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.Amb_1603 , Protein.MC.289_T1.Amb_1603"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T1_Amb_1609 <- scatter_plot(df, "MC.289_T1.Amb_1609", "B", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.Amb_1609 , Protein.MC.289_T1.Amb_1609"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T1_HiT_2023 <- scatter_plot(df, "MC.289_T1.HiT_2023", "C", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.HiT_2023 , Protein.MC.289_T1.HiT_2023"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T1_HiT_2878 <- scatter_plot(df, "MC.289_T1.HiT_2878", "D", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.HiT_2878 , Protein.MC.289_T1.HiT_2878"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T3_Amb_1595 <- scatter_plot(df, "MC.289_T3.Amb_1595", "E", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.Amb_1595 , Protein.MC.289_T3.Amb_1595"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T3_Amb_2741 <- scatter_plot(df, "MC.289_T3.Amb_2741", "F", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.Amb_2741 , Protein.MC.289_T3.Amb_2741"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T3_HiT_2058 <- scatter_plot(df, "MC.289_T3.HiT_2058", "G", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.HiT_2058 , Protein.MC.289_T3.HiT_2058"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T3_HiT_2183 <- scatter_plot(df, "MC.289_T3.HiT_2183", "H", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.HiT_2183 , Protein.MC.289_T3.HiT_2183"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T5_Amb_1721 <- scatter_plot(df, "MC.289_T5.Amb_1721", "I", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.Amb_1721 , Protein.MC.289_T5.Amb_1721"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T5_Amb_2874 <- scatter_plot(df, "MC.289_T5.Amb_2874", "J", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.Amb_2874 , Protein.MC.289_T5.Amb_2874"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T5_HiT_1341 <- scatter_plot(df, "MC.289_T5.HiT_1341", "K", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.HiT_1341 , Protein.MC.289_T5.HiT_1341"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
T5_HiT_2998 <- scatter_plot(df, "MC.289_T5.HiT_2998", "L", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.HiT_2998 , Protein.MC.289_T5.HiT_2998"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
Field_289_1 <- scatter_plot(df, "MC.289_Field_289.1", "M", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_Field_289.1 , Protein.MC.289_Field_289.1"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
Field_289_2 <- scatter_plot(df, "MC.289_Field_289.2", "N", text.scale)
## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_Field_289.2 , Protein.MC.289_Field_289.2"
## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4
out.dir <- "interactive_html_plots"
dir.create(out.dir, showWarnings=FALSE)
saveWidget(ggplotly(T1_Amb_1603), file=paste(out.dir,"prot_vs_trans.T1_Amb_1603.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T1_Amb_1609), file=paste(out.dir,"prot_vs_trans.T1_Amb_1609.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T1_HiT_2023), file=paste(out.dir,"prot_vs_trans.T1_HiT_2023.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T1_HiT_2878), file=paste(out.dir,"prot_vs_trans.T1_HiT_2878.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T3_Amb_1595), file=paste(out.dir,"prot_vs_trans.T3_Amb_1595.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T3_Amb_2741), file=paste(out.dir,"prot_vs_trans.T3_Amb_2741.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T3_HiT_2058), file=paste(out.dir,"prot_vs_trans.T3_HiT_2058.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T3_HiT_2183), file=paste(out.dir,"prot_vs_trans.T3_HiT_2183.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T5_Amb_1721), file=paste(out.dir,"prot_vs_trans.T5_Amb_1721.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T5_Amb_2874), file=paste(out.dir,"prot_vs_trans.T5_Amb_2874.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T5_HiT_1341), file=paste(out.dir,"prot_vs_trans.T5_HiT_1341.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(T5_HiT_2998), file=paste(out.dir,"prot_vs_trans.T5_HiT_2998.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(Field_289_1), file=paste(out.dir,"prot_vs_trans.Field_289_1.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
saveWidget(ggplotly(Field_289_2), file=paste(out.dir,"prot_vs_trans.Field_289_2.scatter.html", sep='/'))
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
## the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
## variable into a factor?
## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
## If you'd like to see this geom implemented,
## Please open an issue with your example code at
## https://github.com/ropensci/plotly/issues
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width
ggarrange(T1_Amb_1603 + rremove("legend"),
T1_Amb_1609 + rremove("legend"),
T1_HiT_2023 + rremove("legend"),
T1_HiT_2878 + rremove("legend"),
T3_Amb_1595 + rremove("legend"),
T3_Amb_2741 + rremove("legend"),
T3_HiT_2058 + rremove("legend"),
T3_HiT_2183 + rremove("legend"),
T5_Amb_1721 + rremove("legend"),
T5_Amb_2874 + rremove("legend"),
T5_HiT_1341 + rremove("legend"),
T5_HiT_2998 + rremove("legend"),
Field_289_1 + rremove("legend"),
Field_289_2 + rremove("legend"),
ncol = 4, nrow = 4)
sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-apple-darwin18.7.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /usr/local/Cellar/openblas/0.3.18/lib/libopenblasp-r0.3.18.dylib
## LAPACK: /usr/local/Cellar/r/4.1.2/lib/R/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] htmlwidgets_1.6.1 plotly_4.10.0 ggpubr_0.4.0 RColorBrewer_1.1-3
## [5] ggtext_0.1.2 ggpmisc_0.5.2 ggpp_0.5.0 ggplot2_3.4.0
## [9] reshape2_1.4.4 dplyr_1.0.10 tibble_3.1.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.9 lattice_0.20-45 confintr_0.2.0 tidyr_1.2.1
## [5] assertthat_0.2.1 digest_0.6.29 utf8_1.2.2 R6_2.5.1
## [9] plyr_1.8.7 backports_1.4.1 MatrixModels_0.5-1 evaluate_0.17
## [13] highr_0.9 httr_1.4.4 pillar_1.8.1 rlang_1.0.6
## [17] lazyeval_0.2.2 rstudioapi_0.14 data.table_1.14.2 SparseM_1.81
## [21] car_3.1-0 jquerylib_0.1.4 Matrix_1.5-1 rmarkdown_2.17
## [25] splines_4.1.2 polynom_1.4-1 stringr_1.4.1 munsell_0.5.0
## [29] gridtext_0.1.5 broom_1.0.1 compiler_4.1.2 xfun_0.33
## [33] pkgconfig_2.0.3 htmltools_0.5.4 tidyselect_1.2.0 viridisLite_0.4.1
## [37] fansi_1.0.3 withr_2.5.0 MASS_7.3-58.1 grid_4.1.2
## [41] jsonlite_1.8.2 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3
## [45] magrittr_2.0.3 scales_1.2.1 cli_3.4.1 stringi_1.7.8
## [49] cachem_1.0.6 carData_3.0-5 farver_2.1.1 ggsignif_0.6.3
## [53] xml2_1.3.3 bslib_0.4.0 ellipsis_0.3.2 generics_0.1.3
## [57] vctrs_0.5.2 cowplot_1.1.1 boot_1.3-28 tools_4.1.2
## [61] glue_1.6.2 purrr_0.3.5 crosstalk_1.2.0 abind_1.4-5
## [65] fastmap_1.1.0 survival_3.4-0 yaml_2.3.5 colorspace_2.0-3
## [69] rstatix_0.7.0 knitr_1.40 sass_0.4.2 quantreg_5.94